Hi Martin, more recent version no longer carry this misleading notice in nsd.conf
Since it is pretty much as given that nsd.conf would be customized (in absence of a conf.d), this would regularly trigger the (very annoying) conflict question on upgrades. So in my personal experience, I much prefer packages using conf.d-style configuration, as it makes upgrades much more hassle free for system administrators. I understand that it merging configuration could be an expected behavior, but I think that's a purely operational issue not related to the packaging of nsd. If you don't object, I would close this bug report as fixed or at downgrade it to wishlist. Best regards, Markus